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FF:11842-124H6: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:35, 29 March 2012


Name:mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02-G)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal precursor cell
cell lineNA
companyNA
collaborationClaudio Schneider LNCIB
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0466
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.226
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13507

Jaspar motifP-value
MA0002.20.903
MA0003.10.635
MA0004.10.57
MA0006.10.664
MA0007.10.137
MA0009.10.815
MA0014.10.706
MA0017.10.407
MA0018.24.51159e-4
MA0019.10.784
MA0024.12.2615e-6
MA0025.10.00904
MA0027.10.706
MA0028.12.19344e-5
MA0029.10.301
MA0030.10.276
MA0031.10.512
MA0035.20.0568
MA0038.12.67484e-4
MA0039.20.00441
MA0040.10.784
MA0041.10.45
MA0042.10.961
MA0043.10.00101
MA0046.10.258
MA0047.20.308
MA0048.10.747
MA0050.10.0251
MA0051.10.171
MA0052.10.478
MA0055.10.301
MA0057.10.934
MA0058.10.168
MA0059.10.574
MA0060.14.59898e-12
MA0061.10.545
MA0062.21.19001e-13
MA0065.20.0895
MA0066.10.808
MA0067.10.355
MA0068.10.494
MA0069.10.082
MA0070.10.835
MA0071.10.554
MA0072.10.294
MA0073.10.197
MA0074.10.48
MA0076.12.87759e-8
MA0077.10.906
MA0078.10.682
MA0079.20.0805
MA0080.24.53779e-7
MA0081.10.00171
MA0083.10.00324
MA0084.10.196
MA0087.10.436
MA0088.10.59
MA0090.13.29974e-5
MA0091.10.487
MA0092.10.532
MA0093.10.621
MA0099.21.21137e-9
MA0100.10.435
MA0101.10.216
MA0102.20.595
MA0103.10.0157
MA0104.20.116
MA0105.10.683
MA0106.10.0936
MA0107.10.163
MA0108.20.0107
MA0111.10.36
MA0112.20.051
MA0113.10.286
MA0114.10.0742
MA0115.10.00908
MA0116.10.602
MA0117.10.727
MA0119.10.0462
MA0122.10.14
MA0124.10.428
MA0125.10.0564
MA0131.10.216
MA0135.10.484
MA0136.18.69594e-10
MA0137.20.13
MA0138.20.745
MA0139.10.618
MA0140.10.825
MA0141.10.254
MA0142.10.0776
MA0143.10.438
MA0144.10.394
MA0145.10.709
MA0146.10.498
MA0147.10.225
MA0148.10.179
MA0149.10.312
MA0150.10.0981
MA0152.10.0605
MA0153.10.876
MA0154.10.716
MA0155.10.118
MA0156.12.79347e-7
MA0157.10.427
MA0159.10.541
MA0160.10.3
MA0162.10.0427
MA0163.10.408
MA0164.10.444
MA0258.10.516
MA0259.10.277



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13507

Novel motifP-value
10.862
100.533
1000.315
1010.0954
1020.147
1030.917
1040.99
1050.178
1060.0677
1070.159
1080.484
1090.989
110.787
1100.35
1110.35
1120.266
1130.0402
1140.181
1150.194
1160.343
1170.635
1180.638
1190.318
120.225
1200.532
1210.894
1220.0304
1230.0621
1240.565
1250.356
1260.598
1270.162
1280.251
1290.764
130.82
1300.783
1310.0227
1320.969
1330.483
1340.317
1350.298
1360.292
1370.295
1380.697
1390.144
140.278
1400.298
1410.976
1420.378
1430.0605
1440.256
1450.576
1460.569
1470.0723
1480.64
1490.0308
150.291
1500.33
1510.269
1520.067
1530.711
1540.906
1557.78399e-4
1560.487
1570.693
1580.177
1590.518
160.0817
1600.244
1610.561
1620.422
1630.0573
1640.0441
1650.882
1660.0664
1670.719
1680.493
1690.267
170.257
180.0683
190.133
20.445
200.165
210.165
220.63
230.00639
240.853
250.11
260.555
270.706
280.361
290.724
30.503
300.576
310.689
321.17313e-4
330.79
340.87
350.438
360.272
370.088
380.947
390.325
40.731
400.521
410.558
420.189
430.171
440.777
450.961
460.486
470.359
480.851
490.86
50.221
500.665
510.974
520.697
530.686
540.533
550.116
560.841
570.658
580.138
590.738
60.405
600.495
610.899
620.59
630.253
640.692
650.383
660.0317
670.257
680.677
690.913
70.0901
700.946
710.842
720.861
730.0857
740.0491
750.933
760.618
770.168
780.556
792.4936e-4
80.316
800.664
810.65
820.576
830.841
840.588
857.25998e-4
860.167
870.73
880.693
890.392
90.253
900.0624
910.244
920.0412
930.767
940.368
950.776
960.99
970.108
980.331
990.0382



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13507


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
2394 (ovarian cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0000992 (female gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002118 (right ovary)
0002323 (body cavity)
0002384 (connective tissue)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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